Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3D

Orthogroup ID

OG0003237

Physical Location & Seq

Genomic Coordinates Forward (+)

34789984 .. 34793640

Gene Structure 3657 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3DG320600.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1245 bp

ATGTCTGTAGCATTGGTACGGGTGGTTTCCCCCAACACAAAGGTGTTAAATTGCTTTGGGCTGTTGGATTCATCAAGTTTTGTTTTGGGGGATGGAAGAGCAAAGATGGGTAGGAAGCAGAAACGGGATTCATGCTGTCTGAGTAGCACTTCTGGCTTACAAAGTGAAACCAAATTCCGCATTTTGTCAAGCATGGTAGCCAACCCGGCTGGAGAAATAGCAGTGTCATCGGAACAGAAGGTTTATGATGTGGTGCTGAAGCAGGCAGCCTTAGTGGAGAAGCAGTTGAGGACTAGTGGAGATGATGTTGATGTGAAGCCTGATATTATTCTTCCAGGGAATCTGAGCTTGTTGAGTGAAGCTTATGACAGATGCAGAGAAGTTTGTGCAGAGTATGCCAAGACTTTTTACCTGGGTACTCTGCTTATGACCCCTGAGAGAAGAAGAGCTATCTGGGCAATATATGTGTGGTGTAGAAGAACTGATGAGCTTGTTGATGGGCCTAATGCCTCACACATAACACCACAAGCTTTGGATAGGTGGGAGTCAAGGTTGGAAGATCTTTTCCAAGGTCGTCCATTCGATATGCTTGATGCTGCTTTATCAGATACAGTCACCCAATTTCCTGTTGACATTCAGCCATTCAAGGATATGATAGAGGGGATGAGAATGGACCTTAGGAAATCAATATACAAGAACTTTGATGAACTATACCTCTACTGTTATTATGTTGCCGGGACTGTTGGACTAATGAGTGTTCCAGTCATGGGCATTGCACCTGATTCGCAAGCAACTACAGAGTCTGTATATAATGCTGCATTAGCATTGGGGATTGCGAATCAGCTAACTAACATACTAAGGGATGTTGGAGAAGATGCAAGGAGAGGACGCATTTATTTACCACAGGATGAGCTGGCACAAGCTGGACTTTCTGATGCTGACATATATGCTGGAAAGGTCACAGATAAATGGAGGAGTTTCATGCAGAGTCAGATTAAGAGAGCAAGGATGTTCTTTGATGAGGCAGAGAAAGGAGTCATGGAGCTCAGTGAAGCCAGCAGATGGCCGGTATTGGCGTCCCTACTTTTGTATCGCCAAATATTGGATGAGATAGAAGCTAATGACTACAACAACTTCACAAAAAGGGCTTATGTAAGCAAAGCTAAGAAATTACTTGCTTTGCCTATGGCATATACTAAATCCCTGATTCTGCCATCAAGAACACTTGAAATAAATCGAGCTTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0009507 GO:0009536 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044424 GO:0044444 GO:0044464

KEGG Pathways

Metabolic & Signaling

ko00906 ko01062 ko01100 ko01110 map00906 map01062 map01100 map01110

Pfam Domains

Protein Families

SQS_PSY

Protein Analysis

414

Amino Acids

46.5

Weight (kDa)

6.13

Isoelectric Point (pI)

55.0

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
SQS_PSY	PF00494	131 - 388	3.9e-79	Squalene/phytoene synthase

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0003237)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G17230 AT5G17230 AT5G17230 AT5G17230
fragaria_vesca	FvH4_1g27480 FvH4_6g38780
malus_domestica	MD09G1146800.v1.1 MD09G1281300.v1.1 MD17G1133400.v1.1
prunus_persica	Prupe.3G013200_v2.0.a1 Prupe.3G013200_v2.0.a1 Prupe.3G178500_v2.0.a1
pyrus_communis	pycom09g06720 pycom09g18890 pycom17g12790
rosa_chinensis	RchiOBHm_Chr2g0152351 RchiOBHm_Chr3g0488531
rosa_laevigata	RLG00000020629 RLG00000022946
rosa_multiflora	Rmu_sc0005885.1_g000002 Rmu_sc0019526.1_g000003
rosa_roxburghii	Rroxscaffold_2G00095770 Rroxscaffold_6G00394200
rosa_rugosa	Rorug02G0432500 Rorug03G0238700 Rorug03G0238800 Rorug03G0238900 Rorug03G0239000
rosa_samantha	Rh2AG494000 Rh2BG506300 Rh2CG480300 Rh2DG517400 Rh3AG287700 Rh3CG321800 Rh3DG320600
rosa_wichuraiana	Rw2G040650 Rw3G025470

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB7I	CCANNNNNTGG	2 cut(s)	1062, 1102
AciI	CCGC	1 cut(s)	178
AcoI	YGGCCR	1 cut(s)	1064
AcsI	RAATTY	1 cut(s)	173
AcuI	CTGAAG	1 cut(s)	278
AcyI	GRCGYC	1 cut(s)	1076
AfaI	GTAC	2 cut(s)	18, 418
AfiI	CCNNNNNNNGG	3 cut(s)	767, 1062, 1102
AgsI	TTSAA	2 cut(s)	646, 1229
AhlI	ACTAGT	1 cut(s)	293
AjnI	CCWGG	2 cut(s)	334, 411
AleI	CACNNNNGTG	1 cut(s)	41
Alw21I	GWGCWC	1 cut(s)	1047
AlwNI	CAGNNNCTG	1 cut(s)	803
AoxI	GGCC	2 cut(s)	500, 1064
ApeKI	GCWGC	3 cut(s)	266, 596, 815
ApoI	RAATTY	1 cut(s)	173
AspS9I	GGNCC	2 cut(s)	500, 673
AsuC2I	CCSGG	2 cut(s)	206, 736
AsuHPI	GGTGA	1 cut(s)	607
AvaII	GGWCC	1 cut(s)	673
AxyI	CCTNAGG	1 cut(s)	677
BaeI	ACNNNNGTAYC	2 cut(s)	1073, 1106
BanII	GRGCYC	1 cut(s)	1047
Bbv12I	GWGCWC	1 cut(s)	1047
BbvI	GCAGC	3 cut(s)	278, 583, 802
BccI	CCATC	5 cut(s)	86, 100, 491, 1056, 1222
BcgI	CGANNNNNNTGC	4 cut(s)	210, 244, 765, 799
BciT130I	CCWGG	2 cut(s)	336, 413
BcnI	CCSGG	2 cut(s)	206, 736
BcuI	ACTAGT	1 cut(s)	293
BfaI	CTAG	1 cut(s)	294
BfmI	CTRYAG	2 cut(s)	6, 795
BglI	GCCNNNNNGGC	1 cut(s)	206
BglII	AGATCT	1 cut(s)	559
BisI	GCNGC	3 cut(s)	267, 597, 816
BlsI	GCNGC	3 cut(s)	268, 598, 817
Bme1390I	CCNGG	4 cut(s)	206, 336, 413, 736
Bme18I	GGWCC	1 cut(s)	673
BmgT120I	GGNCC	2 cut(s)	500, 673
BmrFI	CCNGG	4 cut(s)	206, 336, 413, 736
BmsI	GCATC	4 cut(s)	362, 583, 865, 925
BpmI	CTGGAG	1 cut(s)	231
BpuMI	CCSGG	2 cut(s)	206, 736
BsaHI	GRCGYC	1 cut(s)	1076
BsaJI	CCNNGG	3 cut(s)	335, 412, 568
BsaXI	ACNNNNNCTCC	6 cut(s)	269, 291, 299, 321, 536, 566
Bsc4I	CCNNNNNNNGG	3 cut(s)	767, 1062, 1102
Bse118I	RCCGGY	1 cut(s)	1066
Bse1I	ACTGG	1 cut(s)	761
Bse21I	CCTNAGG	1 cut(s)	677
Bse3DI	GCAATG	1 cut(s)	771
BseBI	CCWGG	2 cut(s)	336, 413
BseDI	CCNNGG	3 cut(s)	335, 412, 568
BseGI	GGATG	6 cut(s)	97, 669, 868, 913, 1014, 1111
BseLI	CCNNNNNNNGG	3 cut(s)	767, 1062, 1102
BseMI	GCAATG	1 cut(s)	771
BseMII	CTCAG	4 cut(s)	131, 335, 426, 1060
BseNI	ACTGG	1 cut(s)	761
BseRI	GAGGAG	1 cut(s)	988
BseXI	GCAGC	3 cut(s)	278, 583, 802
BsgI	GTGCAG	1 cut(s)	408
BshFI	GGCC	2 cut(s)	502, 1066
BsiHKAI	GWGCWC	1 cut(s)	1047
BsiSI	CCGG	3 cut(s)	206, 735, 1067
BslFI	GGGAC	2 cut(s)	751, 1063
BslI	CCNNNNNNNGG	3 cut(s)	767, 1062, 1102
BsmFI	GGGAC	2 cut(s)	751, 1063
BsnI	GGCC	2 cut(s)	502, 1066
Bsp1286I	GDGCHC	1 cut(s)	1047
Bsp143I	GATC	1 cut(s)	559
BspACI	CCGC	1 cut(s)	178
BspANI	GGCC	2 cut(s)	502, 1066
BspCNI	CTCAG	4 cut(s)	132, 336, 427, 1059
BspQI	GCTCTTC	2 cut(s)	91, 439
BsrDI	GCAATG	1 cut(s)	771
BsrFI	RCCGGY	1 cut(s)	1066
BsrI	ACTGG	1 cut(s)	761
BssAI	RCCGGY	1 cut(s)	1066
BssECI	CCNNGG	3 cut(s)	335, 412, 568
BssMI	GATC	1 cut(s)	559
BssNI	GRCGYC	1 cut(s)	1076
BssT1I	CCWWGG	1 cut(s)	568
Bst2UI	CCWGG	2 cut(s)	336, 413
Bst4CI	ACNGT	3 cut(s)	613, 722, 742
Bst6I	CTCTTC	2 cut(s)	91, 439
BstACI	GRCGYC	1 cut(s)	1076
BstAPI	GCANNNNNTGC	1 cut(s)	395
BstC8I	GCNNGC	4 cut(s)	264, 789, 915, 1057
BstDEI	CTNAG	9 cut(s)	140, 271, 344, 435, 677, 857, 1046, 1164, 1242
BstF5I	GGATG	6 cut(s)	97, 669, 868, 913, 1014, 1111
BstKTI	GATC	1 cut(s)	562
BstMBI	GATC	1 cut(s)	559
BstMWI	GCNNNNNNNGC	5 cut(s)	153, 206, 395, 455, 821
BstNI	CCWGG	2 cut(s)	336, 413
BstSCI	CCNGG	4 cut(s)	204, 334, 411, 734
BstSFI	CTRYAG	2 cut(s)	6, 795
BstV1I	GCAGC	3 cut(s)	278, 583, 802
BstX2I	RGATCY	1 cut(s)	559
BstYI	RGATCY	1 cut(s)	559
Bsu36I	CCTNAGG	1 cut(s)	677
BsuRI	GGCC	2 cut(s)	502, 1066
BtsCI	GGATG	6 cut(s)	97, 669, 868, 913, 1014, 1111
BtsI	GCAGTG	1 cut(s)	228
BtsIMutI	CAGTG	2 cut(s)	228, 1054
Cac8I	GCNNGC	4 cut(s)	264, 789, 915, 1057
CaiI	CAGNNNCTG	1 cut(s)	803
Cfr10I	RCCGGY	1 cut(s)	1066
Cfr13I	GGNCC	2 cut(s)	500, 673
CseI	GACGC	2 cut(s)	897, 1065
Csp6I	GTAC	2 cut(s)	17, 417
CspCI	CAANNNNNGTGG	2 cut(s)	513, 548
CviAII	CATG	5 cut(s)	132, 193, 766, 982, 1039
CviQI	GTAC	2 cut(s)	17, 417
DdeI	CTNAG	9 cut(s)	140, 271, 344, 435, 677, 857, 1046, 1164, 1242
DpnI	GATC	1 cut(s)	561
DpnII	GATC	1 cut(s)	559
EaeI	YGGCCR	1 cut(s)	1064
Eam1104I	CTCTTC	2 cut(s)	91, 439
EarI	CTCTTC	2 cut(s)	91, 439
Ecl136II	GAGCTC	1 cut(s)	1045
Eco130I	CCWWGG	1 cut(s)	568
Eco24I	GRGCYC	1 cut(s)	1047
Eco47I	GGWCC	1 cut(s)	673
Eco53kI	GAGCTC	1 cut(s)	1045
Eco57I	CTGAAG	1 cut(s)	278
Eco81I	CCTNAGG	1 cut(s)	677
EcoICRI	GAGCTC	1 cut(s)	1045
EcoRII	CCWGG	2 cut(s)	334, 411
EcoT14I	CCWWGG	1 cut(s)	568
EcoT38I	GRGCYC	1 cut(s)	1047
ErhI	CCWWGG	1 cut(s)	568
FaeI	CATG	5 cut(s)	135, 196, 769, 985, 1042
FalI	AAGNNNNNCTT	2 cut(s)	912, 944
FaqI	GGGAC	2 cut(s)	751, 1063
FatI	CATG	5 cut(s)	131, 192, 765, 981, 1038
Fnu4HI	GCNGC	3 cut(s)	267, 597, 816
FokI	GGATG	6 cut(s)	104, 676, 875, 920, 1021, 1118
FriOI	GRGCYC	1 cut(s)	1047
Fsp4HI	GCNGC	3 cut(s)	267, 597, 816
FspBI	CTAG	1 cut(s)	294
GluI	GCNGC	3 cut(s)	267, 597, 816
GsuI	CTGGAG	1 cut(s)	231
HaeIII	GGCC	2 cut(s)	502, 1066
HapII	CCGG	3 cut(s)	206, 735, 1067
HgaI	GACGC	2 cut(s)	897, 1065
Hin1I	GRCGYC	1 cut(s)	1076
Hin1II	CATG	5 cut(s)	135, 196, 769, 985, 1042
HincII	GTYRAC	1 cut(s)	631
HindII	GTYRAC	1 cut(s)	631
HindIII	AAGCTT	2 cut(s)	360, 528
HpaII	CCGG	3 cut(s)	206, 735, 1067
HphI	GGTGA	1 cut(s)	607
Hpy166II	GTNNAC	1 cut(s)	631
Hpy188I	TCNGA	6 cut(s)	141, 232, 345, 607, 934, 993
Hpy188III	TCNNGA	1 cut(s)	1218
Hpy8I	GTNNAC	1 cut(s)	631
HpyAV	CCTTC	1 cut(s)	232
HpyCH4III	ACNGT	3 cut(s)	613, 722, 742
HpyCH4V	TGCA	6 cut(s)	375, 389, 776, 818, 878, 985
HpyF10VI	GCNNNNNNNGC	5 cut(s)	153, 206, 395, 455, 821
HpyF3I	CTNAG	9 cut(s)	140, 271, 344, 435, 677, 857, 1046, 1164, 1242
Hsp92I	GRCGYC	1 cut(s)	1076
Hsp92II	CATG	5 cut(s)	135, 196, 769, 985, 1042
Kzo9I	GATC	1 cut(s)	559
LguI	GCTCTTC	2 cut(s)	91, 439
LmnI	GCTCC	1 cut(s)	1042
Lsp1109I	GCAGC	3 cut(s)	278, 583, 802
LweI	GCATC	4 cut(s)	362, 583, 865, 925
MaeI	CTAG	1 cut(s)	294
MaeIII	GTNAC	2 cut(s)	613, 958
MalI	GATC	1 cut(s)	561
MboI	GATC	1 cut(s)	559
MboII	GAAGA	7 cut(s)	108, 323, 453, 456, 489, 569, 884
MflI	RGATCY	1 cut(s)	559
MhlI	GDGCHC	1 cut(s)	1047
MluCI	AATT	4 cut(s)	49, 173, 620, 1169
MlyI	GAGTC	4 cut(s)	554, 809, 997, 1044
MmeI	TCCRAC	4 cut(s)	45, 534, 724, 847
MnlI	CCTC	7 cut(s)	282, 520, 652, 725, 878, 966, 1015
MseI	TTAA	2 cut(s)	47, 996
MslI	CAYNNNNRTG	1 cut(s)	41
MspI	CCGG	3 cut(s)	206, 735, 1067
MspR9I	CCNGG	4 cut(s)	206, 336, 413, 736
MvaI	CCWGG	2 cut(s)	336, 413
MwoI	GCNNNNNNNGC	5 cut(s)	153, 206, 395, 455, 821
NciI	CCSGG	2 cut(s)	206, 736
NdeII	GATC	1 cut(s)	559
NlaIII	CATG	5 cut(s)	135, 196, 769, 985, 1042
NmuCI	GTSAC	2 cut(s)	613, 958
OliI	CACNNNNGTG	1 cut(s)	41
PciSI	GCTCTTC	2 cut(s)	91, 439
PfeI	GAWTC	6 cut(s)	68, 128, 340, 782, 838, 1207
PflMI	CCANNNNNTGG	2 cut(s)	1062, 1102
PkrI	GCNGC	3 cut(s)	268, 598, 817
PleI	GAGTC	4 cut(s)	553, 808, 996, 1043
PpsI	GAGTC	4 cut(s)	553, 808, 996, 1043
Psp124BI	GAGCTC	1 cut(s)	1047
Psp6I	CCWGG	2 cut(s)	334, 411
PspGI	CCWGG	2 cut(s)	334, 411
PspPI	GGNCC	2 cut(s)	500, 673
PstNI	CAGNNNCTG	1 cut(s)	803
PsuI	RGATCY	1 cut(s)	559
RsaI	GTAC	2 cut(s)	18, 418
RsaNI	GTAC	2 cut(s)	17, 417
RseI	CAYNNNNRTG	1 cut(s)	41
SacI	GAGCTC	1 cut(s)	1047
SapI	GCTCTTC	2 cut(s)	91, 439
SaqAI	TTAA	2 cut(s)	47, 996
SatI	GCNGC	3 cut(s)	267, 597, 816
Sau3AI	GATC	1 cut(s)	559
Sau96I	GGNCC	2 cut(s)	500, 673
SchI	GAGTC	4 cut(s)	554, 809, 997, 1044
ScrFI	CCNGG	4 cut(s)	206, 336, 413, 736
SduI	GDGCHC	1 cut(s)	1047
SfaNI	GCATC	4 cut(s)	362, 583, 865, 925
SfcI	CTRYAG	2 cut(s)	6, 795
SinI	GGWCC	1 cut(s)	673
SmiMI	CAYNNNNRTG	1 cut(s)	41
SpeI	ACTAGT	1 cut(s)	293
Sse9I	AATT	4 cut(s)	49, 173, 620, 1169
SsiI	CCGC	1 cut(s)	178
SspI	AATATT	1 cut(s)	1101
SspMI	CTAG	1 cut(s)	294
SstI	GAGCTC	1 cut(s)	1047
StyD4I	CCNGG	4 cut(s)	204, 334, 411, 734
StyI	CCWWGG	1 cut(s)	568
TaaI	ACNGT	3 cut(s)	613, 722, 742
TaqI	TCGA	2 cut(s)	582, 1237
TasI	AATT	4 cut(s)	49, 173, 620, 1169
TfiI	GAWTC	6 cut(s)	68, 128, 340, 782, 838, 1207
Tru1I	TTAA	2 cut(s)	47, 996
Tru9I	TTAA	2 cut(s)	47, 996
TscAI	CASTG	2 cut(s)	228, 1054
TseFI	GTSAC	2 cut(s)	613, 958
TseI	GCWGC	3 cut(s)	266, 596, 815
Tsp45I	GTSAC	2 cut(s)	613, 958
TspDTI	ATGAA	4 cut(s)	60, 120, 720, 970
TspRI	CASTG	2 cut(s)	228, 1054
Van91I	CCANNNNNTGG	2 cut(s)	1062, 1102
VpaK11BI	GGWCC	1 cut(s)	673
XapI	RAATTY	1 cut(s)	173
XspI	CTAG	1 cut(s)	294

Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.